Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus

Abstract

Abstract.—Haplotype phylogenies based on DNA sequence data are increasingly being used to test traditional species-level taxonomies based onmorphology. However, few studies have critically com-pared species limits based on morphological andDNA data, and the methods used to delimit species using either type of data are only rarely explained. In this paper, we review three approaches for species delimitation (tree-basedwith DNAdata and tree-based and character-basedwith morphologi-caldata)andpropose explicit protocols for each.We then compare species limits inferred fromthese ap-proaches, using morphological and mtDNA data for the Yarrow’s spiny lizard (Sceloporus jarrovii), a traditionally polytypic species from the southwestern United States andMexico. All three approaches support division of S. jarrovii into ve species, but only two species are the same among the three approaches. We nd the greatest support for the ve species that are delimited based on mtDNA data, and we argue that mtDNA data may have important (and previously unappreciated) advan-tages for species delimitation. Because different data and approaches can disagree so extensively, our results demonstrate that the methodology of species delimitation is a critical issue in systemat-ics. [Mitochondrial DNA; molecular systematics; morphological systematics; nested-clade analysis; phylogeography; population genetics; species limits; taxonomy.